A Martini coarse-grained model of the calcein fluorescent dye
نویسندگان
چکیده
منابع مشابه
The MARTINI force field: coarse grained model for biomolecular simulations.
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction le...
متن کاملPolarizable Water Model for the Coarse-Grained MARTINI Force Field
Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarizatio...
متن کاملThe MARTINI Coarse-Grained Force Field: Extension to Proteins.
Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2-3 orders of magnitude larger compared to atomistic simulations, pr...
متن کاملImproved Parameters for the Martini Coarse-Grained Protein Force Field.
The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. H...
متن کاملDevelopment of a coarse-grained α-chitin model on the basis of MARTINI forcefield.
At nanoscale, atomistic simulation is widely used for investigating crystalline chitin fibers, the structural component for many biological materials. However, the longitudinal dimension of naturally occurring chitin fibers exceeds hundreds of nanometer, beyond the investigation range of all-atom simulation due to the limitation of computational power. Under this context, coarse-grained simulat...
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ژورنال
عنوان ژورنال: Journal of Physics D: Applied Physics
سال: 2018
ISSN: 0022-3727,1361-6463
DOI: 10.1088/1361-6463/aad4b8